Multilayer superstructures based on stacked layered nanomaterials offer the possibility to design three-dimensional (3D) nanopores with highly specific properties analogous to protein channels. In a layer-by-layer design and stacking, analogous to molecular printing, superstructures with lock-and-key molecular nesting and transport characteristics could be prepared. To examine this possibility, we use molecular dynamics simulations to study electric field-driven transport of ions through stacked porous graphene flakes. First, highly selective, tunable, and correlated passage rates of monovalent atomic ions through these superstructures are observed in dependence on the ion type, nanopore type, and relative position and dynamics of neighboring porous flakes. Next, enantioselective molecular transport of ionized l- and d-leucine is observed in graphene stacks with helical nanopores. The outlined approach provides a general scheme for synthesis of functional 3D superstructures.Keywords: enantioselectivity; molecular dynamics simulations; Molecular transport; multilayer graphene nanopores;

Combining biomolecules such as enzymes with nanoparticles has much to offer for creating next generation synergistically functional bionanomaterials. However, almost nothing is known about how these two disparate components interact at this critical biomolecular-materials interface to give rise to improved activity and emergent properties. Here we examine how the nanoparticle surface can influence and increase localized enzyme activity using a designer experimental system consisting of trypsin proteolysis acting on peptide-substrates displayed around semiconductor quantum dots (QDs). To minimize the complexity of analyzing this system, only the chemical nature of the QD surface functionalizing ligands were modified. This was accomplished by synthesizing a series of QD ligands that were either positively or negatively charged, zwitterionic, neutral, and with differing lengths. The QDs were then assembled with different ratios of dye-labeled peptide substrates and exposed to trypsin giving rise to progress curves that were monitored by Förster resonance energy transfer (FRET). The resulting trypsin activity profiles were analyzed in the context of detailed molecular dynamics simulations of key interactions occurring at this interface. Overall, we find that a combination of factors can give rise to a localized activity that was 35-fold higher than comparable freely diffusing enzyme–substrate interactions. Contributing factors include the peptide substrate being prominently displayed extending from the QD surface and not sterically hindered by the longer surface ligands in conjunction with the presence of electrostatic and other productive attractive forces between the enzyme and the QD surface. An intimate understanding of such critical interactions at this interface can produce a set of guidelines that will allow the rational design of next generation high-activity bionanocomposites and theranostics.Keywords: catalysis; enzyme; Michaelis−Menten; nanotechnology; quantum dot;

Using molecular dynamics simulations, we reveal ion rectification in charged nanocones with exit diameters of 1–2 nm. The simulations exhibit an opposite rectification current direction than experiments performed in conical channels with exit diameters larger than 5 nm. This can be understood by the fact that in ultranarrow charged cones screening ions are trapped close to the cone tip at both field directions, which necessitates them to be released from the cone in a correlated multi-ion fashion. Electroosmosis induced by a unidirectional ion flow is also observed.

We use hybrid quantum and classical modeling to describe recently observed molecular sensing at graphene grain boundaries and electrochemical reduction of carbon dioxide (CO2) on molybdenum disulphide (MoS2) flakes. In the sensing studies, classical and quantum molecular dynamics simulations are used to relax graphene with grain boundaries deposited on amorphous SiO2. Electronic structure calculations show how this graphene is locally doped by the substrate and adsorbed molecules, while electronic transport modelling reveals that the doping can lead to synchronous opening and closing of local electron transport channels, resulting in a very large observed sensitivity. In the catalysis studies, electronic structure calculations combined with ab initio molecular dynamics uncover that the metallic character and high d-electron density of molybdenum-terminated MoS2 edges and EMIM-ion delivery are responsible for the observed superior CO2 reduction performance, with a high current density and low ∼54 mV overpotential. The described mechanisms open up new pathways for the design of nanometer-scale highly sensitive chemical detectors and the development of inexpensive systems of CO2 conversion to energy-rich products. These studies illustrate how hybrid modeling techniques can explain complex transport phenomena in nanostructures.

Using in situ liquid cell transmission electron microscopy (TEM), we visualized a stepwise self-assembly of surfactant-coated and hydrated gold nanoparticles (NPs) into linear chains or branched networks. The NP binding is facilitated by linker molecules, ethylenediammonium, which form hydrogen bonds with surfactant molecules of neighboring NPs. The observed spacing between bound neighboring NPs, ∼15 Å, matches the combined length of two surfactants and one linker molecule. Molecular dynamics simulations reveal that for lower concentrations of linkers, NPs with charged surfactants cannot be fully neutralized by strongly binding divalent linkers, so that NPs carry higher effective charges and tend to form chains, due to poor screening. The highly polar NP surfaces polarize and partly immobilize nearby water molecules, which promotes NPs binding. The presented experimental and theoretical approach allows for detail observation and explanation of self-assembly processes in colloidal nanosystems.Keywords: in situ TEM; nanoparticle; nanoparticle chains; self-assembly

Experiments and computer simulations provide a new perspective that strong correlations of counterions with charged nanoparticles can influence the localization of nanoparticles at liquid–liquid interfaces and support the formation of voltage-tunable nanoparticle arrays. We show that ion condensation onto charged nanoparticles facilitates their transport from the aqueous-side of an interface between two immiscible electrolyte solutions to the organic-side, but contiguous to the interface. Counterion condensation onto the highly charged nanoparticles overcomes the electrostatic barrier presented by the low permittivity organic material, thus providing a mechanism to transport charged nanoparticles into organic phases with implications for the distribution of nanoparticles throughout the environment and within living organisms. After transport, the nanoparticles assemble into a two-dimensional (2D) nearly close-packed array on the organic side of the interface. Voltage-tunable counterion-mediated interactions between the nanoparticles are used to control the lattice spacing of the 2D array. Tunable nanoparticle arrays self-assembled at liquid interfaces are applicable to the development of electro-variable optical devices and active elements that control the physical and chemical properties of liquid interfaces on the nanoscale.

We disclose by classical molecular dynamics simulations the formation of long polarization chains induced by ions solvated in a water monolayer confined between graphene sheets. First, we examine the dynamics of confined pure water clusters with Nw < 100 at temperatures of 200–300 K. We show that for certain “magic” Nw the clusters form crystallites with stable structures, where discrete water rings are self-organized with clockwise or anticlockwise orientations of their dipoles. Next, we show that when ions are hydrated in larger clusters with a “bracketed” crystal structure, they can generate long fluctuating chains of (Nw > 30) polarized waters. The chains generated by opposite charged ions can eventually meet, lock, and stay polarized at room temperatures.

We reveal by classical molecular dynamics simulations electroosmotic flows in thin neutral carbon (CNT) and boron nitride (BNT) nanotubes filled with ionic solutions of hydrated monovalent atomic ions. We observe that in (12,12) BNTs filled with single ions in an electric field, the net water velocity increases in the order of Na+ < K+ < Cl–, showing that different ions have different power to drag water in thin nanotubes. However, the effect gradually disappears in wider nanotubes. In (12,12) BNTs containing neutral ionic solutions in electric fields, we observe net water velocities going in the direction of Na+ for (Na+, Cl–) and in the direction of Cl– for (K+, Cl–). We hypothesize that the electroosmotic flows are caused by different strengths of friction between ions with different hydration shells and the nanotube walls.Keywords: boron nitride nanotubes; carbon nanotubes; electroosmotic flow; momentum transfer; nanoscale transport;

We use atomistic molecular dynamics simulations to reveal the binding mechanisms of therapeutic agents in PEG-ylated micellar nanocarriers (SSM). In our experiments, SSM in buffer solutions can solubilize either ≈11 small bexarotene molecules or ≈6 (2 in low ionic strength buffer) human vasoactive intestinal peptide (VIP) molecules. Free energy calculations reveal that molecules of the poorly water-soluble drug bexarotene can reside at the micellar ionic interface of the PEG corona, with their polar ends pointing out. Alternatively, they can reside in the alkane core center, where several bexarotene molecules can self-stabilize by forming a cluster held together by a network of hydrogen bonds. We also show that highly charged molecules, such as VIP, can be stabilized at the SSM ionic interface by Coulombic coupling between their positively charged residues and the negatively charged phosphate headgroups of the lipids. The obtained results illustrate that atomistic simulations can reveal drug solubilization character in nanocarriers and be used in efficient optimization of novel nanomedicines.

We model the dynamics of ion binding to graphene nanostructures. In order to disclose the likely ion binding dynamics, we first perform scanned single-point DFT calculations of monovalent ions (Na+, Li+, Cl–, F–) at fixed distances above planar graphene-like H-passivated molecules of different shapes and sizes. The scans reveal intriguing details about the ion-nanostructure potential energy and charge transfer surfaces. We correlate these static results with our room-temperature quantum molecular dynamics simulations of the ion–molecule systems, performed in both vacuum and water. Our simulations show that anions either are physisorbed onto the nanostructures or covalently bind at their selected regions, depending on the initial conditions, while cations only physisorb onto them.

We show by molecular dynamics simulations that water nanodroplets can be transported along and around the surfaces of vibrated carbon nanotubes. In our simulations, a nanodroplet with a diameter of ∼4 nm is adsorbed on a (10,0) single-wall carbon nanotube, which is vibrated at one end with a frequency of 208 GHz and an amplitude of 1.2 nm. The generated linearly polarized transverse acoustic waves pass linear momentum to the nanodroplet, which becomes transported along the nanotube with a velocity of ∼30 nm/ns. When circularly polarized waves are passed along the nanotubes, the nanodroplets rotate around them and eventually become ejected from their surfaces when their angular velocity is ∼50 rad/ns.Keywords (keywords): carbon nanotubes; molecular dynamics; nanodroplets; transversal acoustic waves;

We explore microscopic principles governing the self-assembly of colloidal octylamine-coated platinum nanocubes solvated in toluene. Our experiments show that regular nanocubes with an edge length of lRC = 5.5 nm form supercrystals with simple cubic packing, while slightly truncated nanocubes with an edge length of lTC = 4.7 nm tend to arrange in fcc packing. We model by averaged force fields and atomistic molecular dynamics simulations the coupling forces between these nanocrystals. Our detailed analysis shows that the fcc packing, which for cubes has a lower density than simple cubic packing, is favored by the truncated nanocubes due to their Coulombic coupling by multipolar electrostatic fields, formed during charge transfer between the octylamine ligands and the Pt cores.Keywords: charge transfer; molecular dynamics; multipolar coupling; nanocubes; self-assembly

We model stabilization of clusters and lattices of spherical particles with dominant electric and magnetic dipolar coupling, and weak van der Waals coupling. Our analytical results demonstrate that dipolar coupling can stabilize nanoparticle clusters with planar, tubular, Möbius, and other arrangements. We also explain for which parameters the nanoparticles can form lattices with fcc, hcp, sh, sc, and other types of packing. Although these results are valid at different scales, we illustrate that realistic magnetic and semiconducting nanoparticles need to have certain minimum sizes to stabilize at room temperature into nanostructures controlled by dipolar coupling.Keywords: clusters; dipolar coupling; nanostructures; stabilization

We have used coarse-grained molecular dynamics simulations to show that hydrated lipid micelles of preferred sizes and amounts of filling with hydrophobic molecules can be self-assembled on the surfaces of carbon nanotubes. We simulated micelle formation on a hydrated (40,0) carbon nanotube with an open end that was covered with amphiphilic double-headed CH3(CH2)14CH(((CH2OCH2CH2)2(CH2COCH2))2H)2 or single-headed CH3(CH2)14CH2((CH2OCH2CH2)2(CH2COCH2))4H lipids and filled with hexadecane molecules. Once the hexadecane molecules inside the nanotube were pressurized and the lipids on its surface were dragged by the water flowing around it, kinetically stable micelles filled with hexadecane molecules were sequentially formed at the nanotube tip. We investigated the stability of the thus-formed kinetically stable filled micelles and compared them with thermodynamically stable filled micelles that were self-assembled in the solution.

Molecular assemblies of highly PEG-ylated phospholipids are important in many biomedical applications. We have studied sterically stabilized micelles (SSMs) of self-assembled DSPE–PEG2000 in pure water and isotonic HEPES-buffered saline solution. The observed SSM sizes of 2–15 nm largely depend on the solvent and the lipid concentration used. The critical micelle concentration of DSPE–PEG2000 is ∼10 times higher in water than in buffer, and the viscosity of the dispersion dramatically increases with the lipid concentration. To explain the experimentally observed results, we performed atomistic molecular dynamics simulations of solvated SSMs. Our modeling revealed that the observed assemblies have very different aggregation numbers (Nagg ≈ 90 in saline solution and Nagg < 8 in water) because of very different screening of their charged PO4– groups. We also demonstrate that the micelle cores can inflate and their coronas can fluctuate strongly, thus allowing storage and delivery of molecules with different chemistries.

We perform coarse-grained molecular dynamics simulations of self-standing nanoparticle membranes observed in recent experiments (K. E. Mueggenburg et al., Nat. Mater., 2007, 6, 656). In order to make our simulations feasible, we model 2–3 times smaller gold nanoparticles (core radius of rcore ≈ 0.8 nm) covered with alkanethiol ligands (length of lligand ≈ 0.5–2.6 nm). We study the structure, stability, and mechanical properties of these membranes and show that these characteristics are controlled by the ratio of RLC = lligand/rcore. For RLC ≈ 0.6, the ligated nanoparticles form well ordered monolayers with hexagonal packing, in agreement with the experiments (RLC ≈ 0.44). For RLC ≈ 1.6, the nanoparticles form less organized multilayers, which are more stable and flexible. We show that these membranes could potentially form stable capsules for molecular storage and delivery.

PEGylated dendron coils (PDCs) were investigated as a novel potential nanocarrier platform. PDCs self-assembled into micelles at lower CMCs than linear copolymer counterparts by 1–2 orders of magnitude, due to the unique architecture of dendrons. MD simulations also supported thermodynamically favourable self-assembly mediated by dendrons.

We demonstrate by molecular dynamics simulations that carbon nanotubes can activate and guide on their surfaces and in their interiors the self-assembly of planar graphene nanostructures of various sizes and shapes. Nanotubes can induce bending, folding, sliding, and rolling of the nanostructures in vacuum and in the presence of solvent, leading to stable graphene rings, helices, and knots. We investigate the self-assembly conditions and analyze the stability of the formed nanosystems, with numerous possible applications.Keywords: carbon nanotube; graphene; molecular dynamics; nanostructures; self-assembly

We demonstrate by molecular dynamics simulations that graphene sheets could be hosted in the hydrophobic interior of biological membranes formed by amphiphilic phospholipid molecules. Our simulation shows that these hybrid graphene−membrane superstructures might be prepared by forming hydrated micelles of individual graphene flakes covered by phospholipids, which can be then fused with the membrane. Since the phospholipid layers of the membrane electrically isolate the embedded graphene from the external solution, the composite system might be used in the development of biosensors and bioelectronic materials.Keywords: bioelectronics; graphene; graphene composite; lipid membrane; self-assembly

We use molecular dynamics simulations combined with iterative screening to test if one can design mechanically controllable and selective molecular pores. The first model pore is formed by two stacked carbon nanocones connected by aliphatic chains at their open tips, in analogy to aquaporins. It turns out that when one nanocone is gradually rotated with respect to the other, the molecular chains alter the size of the nanopore formed at the cone tips and control the flow rates of liquid pentane through it. The second model pore is formed by two carbon nanotubes joined by a cylindrical structure of antiparallel peptides. By application of a torque to one of the nanotubes, while holding the other, we can reversibly fold the peptides into forward or backward-twisted barrels. We have modified the internal residues in these barrels to make these pores selective and controllable. Eventually, we found a nanopore that in the two folded configurations has very different transmission rates for hydrated NH3 molecules.

We demonstrate by molecular dynamics simulations that water nanodroplets can activate and guide the folding of planar graphene nanostructures. Once the nanodroplets are deposited at selected spots on the planar nanostructure, they can act as catalytic elements that initiate conformational changes and help to overcome deformation barriers associated with them. Nanodroplets can induce rapid bending, folding, sliding, rolling, and zipping of the planar nanostructures, which can lead to the assembly of nanoscale sandwiches, capsules, knots, and rings.

We review our theoretical first-principle studies of carbon nanostructures based on graphene sheets, carbon nanotubes, nanocones and fullerenes that are substitutionally doped with transition metal and nitrogen atoms. The results obtained show that metal doping leads to more stable systems in buckled rather than planar structures. The hybrid structures have low-lying excited states, allowing for catalytic activity, in analogy to metalloporphyrins and metallophthalocyanines, as confirmed in recent experiments with Fe-xN-doped carbon nanotubes. Metal-doped carbon nanocones and nanocapsules based on typical fullerenes manifest remarkable electronic and spin polarizations. Additional doping by boron atoms adjacent to the metals increases their HOMO–LUMO gap, stabilizes their electronic structures and causes that their ground states have higher spin multiplicity, where the spin density is spread over the systems. The metallic sites allow functionalization and potential activation of these nanosystems. The hybrid structures formed can have a broad range of applications in catalysis, molecular electronics, light-harvesting and nanomechanics.

To reduce fuel cell cost, durable and inexpensive electrode catalysts need to be developed to replace precious metal materials, particularly for the electrocatalytic oxygen reduction at cathodes. In this study, we explored the structure and the energetics of Fe-xN (x = 2,4) incorporated into carbon nanotubes and graphene using density functional theory to show that these structures are more stable than iron atoms on nanotubes and that pyridinic structures of Fe-4N are more favorable than pyrrolic structures. EXAFS spectra simulated from the optimized structures show good agreement with results of measurements obtained on arrays of aligned nanotubes doped with iron and nitrogen, which have demonstrated activity toward oxygen-reduction reactions.

We model the self-assembly of superlattices of colloidal semiconducting nanorods horizontally and vertically oriented on material substrates. The models include van der Waals and Coulombic coupling between nanorods with intrinsic electric dipoles and their coupling to the substrates. We also investigate the effect of external electric fields on the self-assembly processes. Our theoretical predictions for stable self-assembled superlattices agree well with the available experimental data.

PEGylated dendron coils (PDCs) were investigated as a novel potential nanocarrier platform. PDCs self-assembled into micelles at lower CMCs than linear copolymer counterparts by 1–2 orders of magnitude, due to the unique architecture of dendrons. MD simulations also supported thermodynamically favourable self-assembly mediated by dendrons.